An Interesting Truth
by RebeccaRoy
Summary: It’s been ten years since there has been much said on one Fox Mulder. When a certain new movie comes out the crew of the X-Files realize they must set a few things straight. Even if that means exposing secrets unknown before now.
1. Chapter 1: The Interview

_Disclaimer:_

_I do not own the characters of the X-Files, these belong to that wonderful little production company called 1013 and the various other that own the X-Files, whoever they are, oh yea, Fox, and stuff, right, anyway. I am however borrowing them, no not to make money but for fun and fun only. _

_Summary:_

_It's been a long time and now John Doggett is able to set the record straight on just what really happened with Mulder and Scully. A re-write of what I came up with years ago._

_So I loved the series but had a really mind blowing idea on how to end the whole thing and make it really work. This is my take on it, it will be mostly cannon and will stick to the timeline of the X-Files right through season eight and nine. However there will be a few differences. Anyway do enjoy, and oh no slash and there will be religious themes too._

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Chapter One: The Interview:

J Edgar Hoover Building February 2013:

John Doggett sat behind his desk and worked a small kink out of his neck. He was no longer a young man and today really did not feel it either. Why had he decided to spar with a few of his agents yesterday? Yes it had been fun but he was no spring chicken, he was fifty two years old after all! He was still tall and lean and his short hair was still brown, sure he dyed it but if a woman could so could he. He was not going to get old without a fight, not he! He felt he had weathered life nicely, he was still good looking, with rugged chiseled features with very few lines on his face. He had intense blue eyes and was clad in a well tailored navy blue suit with silk tie his wife picked out for him.

Yes, John Doggett was married and had been for nearly thirty years now. Unlike the TV series that took on the Occult Crimes Division of the FBI and was liberal with his life he was a very happy family man. His wife was not blond and certainly not named Barbara, as if he wanted a blond, though they could turn his head he really was not a man for blonds. He understood why the show was called the X-Files I mean the OCD of the FBI did not sound right and he still really wanted to get in the heads of those who named his division what they did. Oh yes, he was head of the OC division and he had been for years, ever since Fox Mulder had been abducted and ended up doing what he did.

"Sir your ten am is here." Mary Forum, a tall blond woman in simple black suit with lavender shirt said at the door, "shall I send her in?"

"Sure, oh and…"

"Coffee here sir." Forum said putting the decanter, cups, cream, sugar and cookies on the table by the desk, "anything else sir?"

"No, thank you." Doggett said.

She left and a young woman came into the room, she did not look as if she could be any older than his youngest child, Sara who was barely twenty now. He was surprised to see her in a skirt suit of navy with crisp white shirt, navy hose and high heals. Her dark red hair was tied back in a bun and she was carrying an i-pad and shook his hand. He had not expected her to come dressed so professionally, she was from an alternate online paper and he had not expected this. It was a nice surprise to see she had respect for his office and him.

"I am Madison Grace Smith." Smith said, "everyone calls me Grace sir."

"Please to meet you." Doggett said, "I am John Doggett please have a seat."

"Thank you sir." She said.

"So you are here about what has been going on these past few years." Doggett said.

"Yes sir, I never thought the X-Files to be real sir." Grace replied, "I mean you have the names and look similar to the actors, I mean wow to be here sir."

"You had questions?" Doggett asked.

"Yes sir, how much was true?"

"Eighty percent." Doggett replied, "first off I never lost a son to a murderer, Marcus was never kidnapped and I had two daughters, they are all grown now. My son is now twenty seven and has two kids of his own, I have a daughter, Rachel who is twenty three and my youngest girl Ruth at twenty." Doggett replied.

"Your wife is Gretchen Matsuo, grandparents came over before world war two and her parents were born during that war. No blond for you sir."

"No, she looks sweet and delicate but she keeps me on the straight and narrow." Doggett replied.

"What of Mulder and Scully?"

"Fox and Dana?" Doggett replied.

"Doesn't Mulder hate his first name?"

"Him? No, I mean the puns he came up with that grew old fast." Doggett replied, "oh and those tapes of his? Not porn, he has an unhealthy obsession with Japanese anime, I mean he liked it before it ever took off here in America and he is fluent in Japanese so he can watch them in Japanese."

"So those tapes that he claimed were not his?"

"Not porn, in fact closest he ever got to it was the SI swimsuit issue." Doggett replied. "It's one of his running jokes, Dana would find him reading or watching one of those and he would pretend he was not."

John Doggett had been good friends with Mulder and Scully, er Dana and Fox for a long time. The series showed Mulder as a loner but that was far from the truth, many in the FBI liked him and how he had the knack to solve cases. Even when he went toe to toe with the bosses he was still liked even by them. He was not fighting for himself but for America and for those inside her and that gained respect. He did not hunt down monsters and aliens for himself but to protect his people, the citizens of America. He was a true patriot in every since of the word and would die for his nation and people if it came down to it. He was no politician and cared little for that sort of thing and even those that rose the ranks that did care for that sort of thing could not help but grudgingly admire him for what he stood for.

In fact long ago Doggett had been such an agent, but meeting and becoming friends with Mulder and Scully had changed his mind. He was called in to look for Mulder as Mulder had been a good friend and fellow agent and his skills at tracking were second to none. It helped he already had worked a few cases with both Mulder and Scully and Scully, Dana could tolerate him, sort of. Well she was mad at him at first and nearly, nearly threw the glass of water he offered her into his face (sure that made it to screen on the X-Files) but did not. He even knew before she told him she was pregnant, he recognized the signs from when his wife was and knew how and when to duck. He even introduced Dana to Gretchen who had helped her through her pregnancy. He had learned that both Fox and Dana were married and it was a secret that Skinner kept and had kept for two years. Dana gave birth not in an abandoned town he never heard of but in the hospital under heavy guard with Fox outside pacing the floor with Doggett trying to offer as much support as he could.

"So what can you now tell me about what really went on?" Grace asked.

"Like I said, eighty percent of it was true that you saw on TV." Doggett replied, "but some, well that was not but what was true is that Operation Paper Clip was far more sinister than we thought. Well let me explain, most of those brought over wanted to be here, and wanted to do good, but a small part ended up as part of the Syndicate."

"I see, and that part is fully true, were do the aliens and stuff come in?"

"Best place to start really is when Fox got kidnapped…"

"You mean abducted."

"No I mean kidnapped."

"Very well, tell me what happened then."

Doggett remembered back to what Fox had told him all those years ago when he came back. He had not wanted to believe him but the truth was before him and he had learned so much from that. Truths that shocked and scared him and made him angry and humbled all at once. He took a breath and began to tell all about the day that Fox Mulder was kidnapped and taken away by the aliens, and not for the reason that anyone would have expected at all.

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_So there we go, first chapter and one that has been bouncing around my head for a while. It gets really shocking the more we go on, but you will have to go to the next chapter find out._

_Oh, and I always thought Fox Mulder should have embraced his first name. The puns, oh the puns he could have fun with that name! Yes here he did, and yes some got him in a headlock more than once when he "helpfully" included Doggett (Doggett loves to spar and would invite Mulder, you can guess what happens with that, marine Vs. Mulder= Mulder in a head lock) who also kicked his ass._

_Oh and I only get paid in reviews, so please do review!_


	2. Chapter 2: The Abduction

Chapter Two: The Abduction:

Unknown Location March 2000:

Time was hard to measure in such a bare cold room. It was all metal with one light that shone down on a single cold metal chair bolted to the floor. A nearly naked man was bound to that chair, hands behind his back bound with metal bands to the chair, feet bound to the legs of the chair. All he wore was his black silk boxers and nothing else and it was clear he was cold because of this. He looked very pale under the harsh light on him, and the only color in this room was his short brown hair with the bangs falling on either side of his face. This was Fox Mulder, recent "victim" of abduction by aliens, those who had captured him did not see him as a victim at all but part of the enemy. It was why he was being held here and why he was about to find out the harsh truth, one that was far more shocking than anything in his imagination.

A woman entered the room, tall, thin with shoulder length blond hair, hazel eyes and pale skin. She was clad in a black skirt suit with white shirt and was hardly alone. A man, or something that looked like a man entered the room with her. He was tall, powerfully built with square jaw, and short brown hair. He was clad in a gray suit with white shirt and blue tie. He did not look happy, for so long the family if this man had tortured, hunted and experimented on innocent peoples, his people to be precise. Ever since that fateful day in late 1947. His was not the only guilty party, there were many others but the Mulders had done so much harm. This ones actions had seemed harmless but he had gotten too close to the truth and if he was the enemy and knew what they were really doing he was going to die.

"So much suffering for my people here." The bounty hunter said, "so many abominations created."

"I am sorry for your pain and loss." Covarrubias replied.

"Doesn't matter, you cannot stop what I can." The bounty hunter said. "I am angry as my people came here to help but were killed and worse."

"I know, I am sorry for that and until last year I had no idea of the truth." Marita said, "I cannot see how you can forgive me for the evil I did."

"You are not to blame, those that fed you lies are, but him, is he like you?" The bounty hunter asked, "he is of the family who caused much pain and suffering to my people."

"Give him the shot, we will soon find out what side he is on." Marita said.

Unlike the TV show Mulder was not hurt, well accept for his pride when he woke fully. No he had been treated thus to throw him off balance and because he was hated and feared among the aliens. He would wake cold and disoriented but there would be no experimentations on him, no cruel chair to bind him and torture him for months on end. The bounty hunter gave him the shot and waited a few moments before he stuck poppers under his nose to wake Mulder up. He came awake, drugged and unfocused he looked around trying to clear his head but unable to. He felt as if he were in a dream, everything was fuzzy and he felt almost warm and content.

"What is your name?" Marita asked.

"Fox William Mulder." Mulder replied.

"Date of birth."

"October 13, 1961."

"Where do you work."

"FBI OC division, funny name that, show has it right X-Files much better, OCD who thought that was a…"

"What do you know of the syndicate?" The bounty hunter asked.

"They are helping with an alien invasion. The black oil ties to this, infects innocent, want to make us our slaves."

"Who does?" The bounty hunter growled.

"You do, you come, kill clones and faceless rebels, rebels ones who want to stop the colonization." Mulder replied. "To be finished 12/21/2012, we all die then, no worse than death, slavery for all."

"Do you wish for this slavery Mulder?" The bounty hunter spat, showing the hint of anger under the surface.

"No, I want my people free, let my people go, great man said that long ago, but pharaoh refused, but God does not like us now, hates us, lets you take us and anal probe and other things."

"I think we got our answers." Marita said, "now what?"

"Leave him here, for now."

"But…"

"Leave him!"

The bounty hunter left the light and the room with Marita following him. It was rare to get any emotional response from him, but she could feel the anguish deep below the surface. He might be alien and have powers and such she never could but at the end of the day he was as mortal and as feeling as she was. He was looking beyond the bulkhead of the room seeing something she could not far away. When he spoke his voice had a hint of pain in it, very faint but one she could detect and it cut her to the core. He was not a soulless killer, not at all, but a being who was doing what he believed was right.

"You know that long ago for you, before you were born my people found the purity on your world, we were surprised that it had made it here, we have removed it well on other worlds. We sent our best scientist but something went wrong, they were spotted and the craft shot down."

"Wait what of the craft in Antarctica that was found, that was ancient…"

"No, planted, many such are by the syndicate, they heard the air force found the craft in Roswell and took it and our now dead scientist and that man, your family helped create abominations with them!"

"Our family was a good family before father and uncle and cousin did what they did." Marita replied, "you know not all of us are like those in the syndicate, you promised to give us one more chance, is that not why you kidnapped Fox?"

"If he will help us then he lives, if not than he will die…"

Marita was in fact Mulder's sister, she had been taken at a young age to keep William and Tina in line. They had ideas that did not go well with the Syndicate, in fact they were trying to create their own power base not for good but to make themselves the "gods" of this world. They were not nice people and had thought their only daughter dead and so stayed in line with the program. Even Tina did and would help in stringing along her son to keep him from the truth, she was every bit as evil as her husband and in fact had helped create the clones in the first place. When William had wanted to tell Fox everything she had Krycek go and kill him. Then she was going to have him killed but the black lunged bastard had fumbled that up. Now this loose canon was out there and she was not happy about it.

Marita had been raised by a Syndicate family loyal to what they believed was the fight against aliens. She was raised with love and did not remember her early years at all. In fact she never would have if not for the purity infecting her and her memories coming back. She had remembered the fights of her parents and the full truth, with cunning she had acted as if she still was loyal to the Syndicate but sot out the aliens. She was surprised when they agreed to meet her and after a tense first meeting realized she was against everything the Syndicate stood for. Now she was working to help bring down the remainder of the Syndicate. She had helped a few years ago when the majority of the syndicate was killed by "faceless rebels" who were shape-shifters like the bounty hunter. Everyone had died in that hanger, everyone but the children who were taken to safety.

Marita had believed all the lies of the Syndicate at one time, the lies that there was a colonization, that the aliens were the enemy. But no more, she was angry and wanted revenge, more so as the death of her adoptive parents was not by aliens at all but by clones created to make it look like aliens. She had been fooled for so long she was not happy about that at all. Now she was here, fighting the evil Syndicate and making damn sure that 12/21/2012 was a normal day for all. She was glad to learn that her brother was not involved in the Syndicate at all and was in fact against it. The bounty hunter was too though he did not fully show it, he had an image to keep after all. He injected Mulder and unbound him and stepped back letting him wake up fully and look around confused.

"What, where am I?" He asked.

"Safe, glad to know you don't support the Syndicate." Marita said, "everything you know about the aliens is lies."

"What do you mean, they want to colonize us!" Mulder snapped back.

"No, we came to remove the purity but some of your people took the bodies of Cal and Rill and desecrated them!" The bounty hunter said showing a bit of the deep pain he felt, "they came to help and were used in evil experiments by evil men, your father and uncle were part of that and I curse them, though not you."

Mulder knew he had a choice to make, he wanted the truth, always had and stood, taking the blanket offered and wrapping himself in it. He looked from Marita to the bounty hunter and realized they thought him the enemy, but for different reasons than he would have thought. He wanted the truth and followed them out, he was allowed to get dressed and taken to another room where Billy Miles sat waiting for him looking as healthy and dare he say happy? What did he have to be happy about? His life had been hell for so long and had started when he was in high school, what then did he have to smile about seeing Mulder here? He stood up and shook Mulder's hand and ushered him to a seat.

"So I am here to see the how far the rabbit hole goes?" Mulder said, "should not be hard, I am a fox…"

"Stop it, not now." Marita said rolling her eyes.

"What, I am foxy…"

"Let's get to work sir, so much truth here, it will anger you but then I think you will see who the real enemy is." Billy said.

"That why you so happy?" Mulder asked.

"Hell yea, the aliens are not the enemy but really cool, they really are, I have met a few of them." Billy said, "aside from ugly here."

"Shut it." The bounty hunter growled.

"Touchy, he has no sense of humor." Billy said turning back to the computer screen, "ready for this?"

"Yea, I want to see the truth for myself." Mulder replied.

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_So yea, you did not think it was going to go there did you? The aliens really are not the bad guys here but as much victims as those preyed on by the syndicate. In fact if the third movie used this twist I would be pleased, it would make since, it really would. _

_Anyway please let me know what you think (no flames though please) and review!_


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